1FHW

Structure of the pleckstrin homology domain from GRP1 in complex with inositol(1,3,4,5,6)pentakisphosphate

• PDB DOI: https://doi.org/10.2210/pdb1FHW/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-08-02 Released: 2000-08-23 
• Deposition Author(s): Ferguson, K.M., Kavran, J.M., Sankaran, V.G., Fournier, E., Isakoff, S.J., Skolnik, E.Y., Lemmon, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.270 
• R-Value Work: 0.229 
• R-Value Observed: 0.229 

Literature

Structural basis for discrimination of 3-phosphoinositides by pleckstrin homology domains

Ferguson, K.M., Kavran, J.M., Sankaran, V.G., Fournier, E., Isakoff, S.J., Skolnik, E.Y., Lemmon, M.A.

(2000) Mol Cell 6: 373-384

• PubMed: 10983984 
• DOI: https://doi.org/10.1016/s1097-2765(00)00037-x
• Primary Citation of Related Structures:  
  1FAO, 1FB8, 1FHW, 1FHX


• PubMed Abstract: 
  

  Pleckstrin homology (PH) domains are protein modules of around 120 amino acids found in many proteins involved in cellular signaling. Certain PH domains drive signal-dependent membrane recruitment of their host proteins by binding strongly and specifically to lipid second messengers produced by agonist-stimulated phosphoinositide 3-kinases (PI 3-Ks). We describe X-ray crystal structures of two different PH domains bound to Ins(1,3,4,5)P4, the head group of the major PI 3-K product PtdIns(3,4,5)P3. One of these PH domains (from Grp1) is PtdIns(3,4,5)P3 specific, while the other (from DAPP1/PHISH) binds strongly to both PtdIns(3,4,5)P3 and its 5'-dephosphorylation product, PtdIns(3,4)P2. Comparison of the two structures provides an explanation for the distinct phosphoinositide specificities of the two PH domains and allows us to predict the 3-phosphoinositide selectivity of uncharacterized PH domains.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics and The Johnson Foundation, University of Pennsylvania School of Medicine, Philadelphia 19104, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 31.69 kDa 
• Atom Count: 2,245 
• Modelled Residue Count: 248 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GUANINE NUCLEOTIDE EXCHANGE FACTOR AND INTEGRIN BINDING PROTEIN HOMOLOG GRP1	A, B	129	Mus musculus	Mutation(s): 0
UniProt
Find proteins for O08967 (Mus musculus) Go to UniProtKB:  O08967

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I5P	C [auth A], E [auth B]	INOSITOL-(1,3,4,5,6)-PENTAKISPHOSPHATE C6 H17 O21 P5 CTPQAXVNYGZUAJ-ADOSBGCESA-N
SO4	D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.270 
• R-Value Work: 0.229 
• R-Value Observed: 0.229 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.97	α = 90
b = 72.22	β = 93.21
c = 46.9	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-08-23 
Deposition Author(s): Ferguson, K.M., Kavran, J.M., Sankaran, V.G., Fournier, E., Isakoff, S.J., Skolnik, E.Y., Lemmon, M.A.

Revision History  

• Version 1.0: 2000-08-23
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance